The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays
Open accessAbstract
RNA binding to high-density oligonucleotide arrays has shown tantalizing differences with solution experiments. We analyze here its sequence specificity, fitting binding affinities to sequence composition in large datasets. Our results suggest that the fluorescent labels interfere with binding, causing a catch-22. To be detected, the RNA must both glow and bind: without labels it cannot be seen even if bound, while with too many it will not bind. A simple model for the binding of labeled oligonucleotides sheds light on the interplay between binding energies and labeling probability.
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Cites
Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection.
Li, C., & Wong, W. H. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.98.1.31 · Cited by 3,133
Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
Sugimoto, N., Nakano, S.-I., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi, T., Yoneyama, M., & Sasaki, M. (1995) · Biochemistry · doi:10.1021/bi00035a029 · Cited by 697
Cited by
From RNA-seq reads to differential expression results
Oshlack, A., Robinson, M. D., & Young, M. D. (2010) · Genome Biology · doi:10.1186/gb-2010-11-12-220 · Cited by 698
A high-resolution map of transcription in the yeast genome
David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C. J., Bofkin, L., Jones, T., Davis, R. W., & Steinmetz, L. M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601091103 · Cited by 697
Removing technical variability in RNA-seq data using conditional quantile normalization
Hansen, K. D., Irizarry, R. A., & WU, Z. (2012) · Biostatistics · doi:10.1093/biostatistics/kxr054 · Cited by 607
Reliability and reproducibility issues in DNA microarray measurements
DRAGHICI, S., KHATRI, P., EKLUND, A., & SZALLASI, Z. (2006) · Trends in Genetics · doi:10.1016/j.tig.2005.12.005 · Cited by 590
Diboun, I., Wernisch, L., Orengo, C. A., & Koltzenburg, M. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-252 · Cited by 592
Metadata
- Authors
- Naef, F., & Magnasco, M. O.
- Venue
- Physical Review E
- Publisher
- American Physical Society (APS)
- Published
- 2003-07-16
- Volume
- 68
- Issue
- 1
- Pages
- 011906-011906
- ISSN
- 1063-651X (ISSN-L)
- 1095-3787
- OpenAlex
- W1978673080
- Cited by
- 201
- References
- 2
- FWCI
- 6.22
- Type
- journal article
- Language
- en
- Open access
- green
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